title: UMARY-880-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-602-CRBLM-mRNA

status: Public on Apr 20 2010

type: RNA

city: Bethesda

first: J Raphael

last: Gibbs

state: MD

address: 35 Convent Drive, Bldg 35/1A1015, MSC3707

department: Computational Biology Core

country: USA

institute: National Institutue on Aging, NIH

description: Human Brain Tissue: CRBLM

hyb_protocol: Illumina Whole Genome Gene Expression

scan_protocol: Illumina Beadstation

data_processing: Beadstudio Gene Expression Module v3.2.7, rank-invariant normalization

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Human Brain Tissue: CRBLM

label_protocol: Illumina Whole Genome Gene Expression

extract_protocol: TRIZOL

tag: gender

value: male

tag: age

tag: pmi

tag: tissuebank

value: UMARY

value: F

tag: tissue

value: cerebellum


title: UMARY-927-CRBLM-mRNA

description: Human Brain Tissue: CRBLM

value: B


title: UMARY-813-CRBLM-mRNA

description: Human Brain Tissue: CRBLM

value: female


title: UMARY-871-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1206-CRBLM-miRNA

description: Human Brain Tissue: CRBLM

hyb_protocol: Illumina Human MicroRNA Expression Universal Arrays

data_processing: Beadstudio Gene Expression Module v3.2.7, quantile normalization

value: L


title: UMARY-1170-CRBLM-miRNA

description: Human Brain Tissue: CRBLM

label_protocol: Illumina Human MicroRNA Expression Universal Arrays


title: UMARY-5081-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-5087-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-879-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1158-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1136-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1133-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1114-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-5028-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1104-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4924-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-5079-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-604-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1079-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-5078-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1078-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4916-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-5024-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: JHU-995-CRBLM-miRNA

description: Human Brain Tissue: CRBLM

value: JHU

value: J


title: UMARY-1065-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: JHU-993-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4915-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4903-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4842-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4788-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: JHU-719-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1076-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4841-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: JHU-712-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: JHU-713-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1465-FCTX-miRNA

description: Human Brain Tissue: FCTX

source_name: Human Brain Tissue: FCTX

value: H

value: frontal cortex


title: UMARY-4786-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: JHU-710-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: JHU-705-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: BLSA-827-CRBLM-miRNA

description: Human Brain Tissue: CRBLM

value: BLSA


title: UMARY-4727-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: BLSA-745-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4726-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4640-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: JHU-384-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: BLSA-2093-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: BLSA-2102-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-5086-CRBLM-mRNA

description: Human Brain Tissue: CRBLM

value: G


title: UMARY-4725-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4598-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4590-CRBLM-mRNA

description: Human Brain Tissue: CRBLM

value: A


title: BLSA-2037-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4729-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4636-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4549-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: BLSA-1961-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: BLSA-1805-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4593-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: BLSA-1640-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: BLSA-1775-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4540-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4543-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4545-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: BLSA-1603-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4542-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4263-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: BLSA-1579-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: BLSA-1595-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: BLSA-2066-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: BLSA-1556-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4789-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1939-CRBLM-miRNA

description: Human Brain Tissue: CRBLM

value: K


title: BLSA-2069-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: BLSA-1924-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: BLSA-2020-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: BLSA-2000-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1935-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1827-CRBLM-miRNA

description: Human Brain Tissue: CRBLM

value: M


title: UMARY-1936-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1917-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1909-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1917-CRBLM-mRNA

description: Human Brain Tissue: CRBLM

value: D


title: UMARY-1940-CRBLM-mRNA

description: Human Brain Tissue: CRBLM

value: male


title: UMARY-1936-CRBLM-mRNA

description: Human Brain Tissue: CRBLM

value: UMARY


title: UMARY-1907-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1903-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1710-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1909-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4782-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1614-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1668-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: BLSA-1883-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1652-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: JHU-994-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1648-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1866-CRBLM-mRNA

description: Human Brain Tissue: CRBLM

value: F


title: UMARY-1902-CRBLM-mRNA

description: Human Brain Tissue: CRBLM

value: cerebellum


title: UMARY-1865-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1584-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1867-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1862-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1578-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1612-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1611-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1613-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1568-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1849-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1571-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1847-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: BLSA-1840-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: BLSA-1839-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1846-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1544-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1545-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1830-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1535-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1827-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1540-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1502-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-5087-CRBLM-miRNA

description: Human Brain Tissue: CRBLM

value: I


title: UMARY-1797-CRBLM-mRNA

description: Human Brain Tissue: CRBLM

value: E


title: UMARY-5086-CRBLM-miRNA

description: Human Brain Tissue: CRBLM

value: female


title: UMARY-1825-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-5081-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1712-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-5024-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1795-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-5079-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1792-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1454-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1713-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1710-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-5078-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1715-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1648-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4916-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4924-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1652-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4915-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4903-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1614-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4842-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1613-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1611-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1583-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1612-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1578-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-927-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4782-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4786-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-914-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4727-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1584-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4729-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4725-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1544-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1545-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1571-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1570-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4640-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1568-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4593-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1535-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4636-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4543-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4598-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4726-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4590-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4841-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: BLSA-2069-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1502-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1465-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4542-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1498-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4545-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: BLSA-2000-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1326-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: BLSA-2020-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1486-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1496-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-142-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1230-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1940-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1260-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4540-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1206-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: BLSA-1838-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1226-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1907-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1454-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1170-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1846-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1849-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1209-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1136-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1158-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: BLSA-1840-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: BLSA-1883-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-142-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: BLSA-1839-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1583-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1134-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1465-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4263-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1326-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1079-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1540-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1114-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4549-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1105-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1133-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1104-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1105-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1028-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1134-CRBLM-miRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1065-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: JHU-995-CRBLM-mRNA

description: Human Brain Tissue: CRBLM

value: JHU

value: C


title: JHU-994-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: JHU-993-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1076-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1037-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: JHU-713-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1209-CRBLM-miRNA

description: Human Brain Tissue: CRBLM

value: H


title: JHU-719-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: JHU-712-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: JHU-705-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: JHU-710-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: BLSA-2093-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: BLSA-2102-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: BLSA-745-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: BLSA-1961-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: BLSA-827-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: BLSA-1775-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: BLSA-1805-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-4590-TCTX-mRNA

description: Human Brain Tissue: TCTX

source_name: Human Brain Tissue: TCTX

value: temporal cortex


title: BLSA-1640-CRBLM-mRNA

description: Human Brain Tissue: CRBLM

value: BLSA


title: BLSA-1603-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: BLSA-1556-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: BLSA-1595-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1064-TCTX-mRNA

description: Human Brain Tissue: TCTX

value: G


title: BLSA-1802-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-602-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: BLSA-1579-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: UMARY-1611-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-1496-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: BLSA-2037-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: BLSA-827-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: BLSA-1924-CRBLM-mRNA

description: Human Brain Tissue: CRBLM


title: BLSA-1556-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: BLSA-1889-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-879-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-914-TCTX-mRNA

description: Human Brain Tissue: TCTX

value: B


title: BLSA-1595-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-880-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-933-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-871-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-5087-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-5086-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-604-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-819-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-5078-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-5079-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-5081-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-927-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-4924-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-4916-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-4903-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-5024-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-5028-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-813-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-4915-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-4789-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-4788-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-4841-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-4725-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-4842-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-4727-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-4726-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-4640-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-4636-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-4543-TCTX-mRNA

description: Human Brain Tissue: TCTX

value: A


title: UMARY-4593-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-4729-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-4545-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-4542-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: BLSA-2069-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-4263-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: BLSA-2020-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-4549-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-1935-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-4598-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: BLSA-2066-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-1917-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-1936-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-4540-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-1902-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-1939-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-1867-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-1940-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-1909-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: BLSA-1883-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: BLSA-2000-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-1903-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-1866-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-1849-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-1862-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-1847-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-1846-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-1865-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: UMARY-4782-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: BLSA-1840-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: BLSA-1839-TCTX-mRNA

description: Human Brain Tissue: TCTX


title: CSR27 stressed replicate 1

city: NEW DELHI

first: Awadhesh

last: Pandit

state: DELHI

address: LBS BUILDING

country: India

institute: NRC ON PLANT BIOTECHNOLOGY

description: Gene expression profile of salt tolerant parent in stress (150mM NaCl treatment for 24 hrs)

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: GCOS 1.2

organism: Oryza sativa Indica Group

source_name: salt tolerant parent in stress conditions

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated by using TRIzol Reagent (Sigma) RNA samples were processed as recommended by Affymetrix (Affymetrix geneChip Expression Analysis Technical manual; Affymetrix)

value: Seedling 10 days after germination

tag: variety

tag: phenotype

value: Salt tolerant


title: ..SAL_IV_2

status: Public on Apr 14 2010

city: Krakow

first: Marcin

last: Piechota

address: Smetna 12

department: Molecular Neuropharmacology

country: Poland

institute: Institute of Pharmacology PAS

description: Replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

organism: Mus musculus

source_name: Striatum of 6-10 week old C57BL/6J mice

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: timepoint

tag: drug

value: Saline

tag: group no.

tag: large batch

value: Y

tag: plate

tag: hybridization batch

value: IV


title: CSR27 stressed replicate 2


title: NIC_IV_2

description: Replicate 2

value: Nicotine


title: CSR27 control replicate 1

description: Gene expression profile of salt tolerant parent in control

source_name: salt tolerant parent in control conditions


title: MI48 stressed replicate 1

description: Gene expression profile of salt sensitive parent in stress (150mM NaCl treatment for 24 hrs)

source_name: salt sensitive parent in stress conditions

value: Salt sensitive


title: MET_I_2

description: Replicate 2

value: Methamphetamine


title: ..SAL_II_2

description: Replicate 2


title: ETOH_II_2

description: Replicate 2

value: Ethanol


title: NIC_II_2

description: Replicate 2


title: CSR27 control replicate 2


title: ..SAL_VIII_2

description: Replicate 2


title: MI48 control replicate 1

description: Gene expression profile of salt sensitive parent in control

source_name: salt sensitive parent in control conditions


title: NIC_I_2

description: Replicate 2


title: ETOH_I_2

description: Replicate 2


title: MI48 control replicate 2


title: ETOH_VIII_2

description: Replicate 2


title: NAIVE_VIII_2

description: Replicate 2

value: Naive


title: MI48 stressed replicate 2


title: MET_VIII_2

description: Replicate 2


title: MET_IV_2

description: Replicate 2


title: UMARY-1078-CRBLM-mRNA

description: Human Brain Tissue: CRBLM

value: female

value: UMARY

value: E

value: cerebellum


title: NAIVE_IV_2

description: Replicate 2


title: NAIVE_II_2

description: Replicate 2


title: MET_II_1

description: Replicate 1


title: NIC_VIII_1

description: Replicate 1


title: UMARY-4786-TCTX-mRNA

description: Human Brain Tissue: TCTX

value: male

value: temporal cortex


title: NIC_IV_1

description: Replicate 1


title: UMARY-1907-TCTX-mRNA

description: Human Brain Tissue: TCTX

value: A


title: NAIVE_I_1

description: Replicate 1


title: NIC_II_1

description: Replicate 1


title: NAIVE_IV_1

description: Replicate 1


title: ..SAL_IV_1

description: Replicate 1


title: ETOH_IV_1

description: Replicate 1


title: ..SAL_I_2

description: Replicate 2


title: MET_I_1

description: Replicate 1


title: NAIVE_VIII_1

description: Replicate 1


title: ETOH_I_1

description: Replicate 1


title: NIC_I_1

description: Replicate 1


title: ..SAL_VIII_1

description: Replicate 1


title: ETOH_VIII_1

description: Replicate 1


title: MET_VIII_1

description: Replicate 1


title: NAIVE_II_1

description: Replicate 1


title: NAIVE_IV_3

description: Replicate 3

value: V


title: MET_VIII_3

description: Replicate 3


title: ETOH_II_1

description: Replicate 1


title: ..SAL_II_1

description: Replicate 1


title: MET_IV_1

description: Replicate 1


title: ..SAL_I_1

description: Replicate 1


title: ..SAL_II_3

description: Replicate 3


title: ETOH_VIII_3

description: Replicate 3


title: NAIVE_II_3

description: Replicate 3


title: MET_IV_3

description: Replicate 3


title: NAIVE_I_2

description: Replicate 2


title: MET_I_3

description: Replicate 3


title: ..SAL_IV_3

description: Replicate 3


title: NAIVE_VIII_3

description: Replicate 3


title: NIC_II_3

description: Replicate 3


title: ETOH_IV_2

description: Replicate 2


title: ..SAL_I_3

description: Replicate 3


title: ETOH_II_3

description: Replicate 3


title: NIC_VIII_3

description: Replicate 3


title: ETOH_I_3

description: Replicate 3


title: NIC_VIII_2

description: Replicate 2


title: NIC_IV_3

description: Replicate 3


title: MET_II_2

description: Replicate 2


title: MF_II_2

description: Replicate 2

value: Morphine

value: X

value: II


title: NAIVE_I_3

description: Replicate 3

value: Y


title: ETOH_IV_3

description: Replicate 3


title: MF_I_2

description: Replicate 2


title: MF_VIII_2

description: Replicate 2


title: MET_II_3

description: Replicate 3


title: ..SAL_VIII_3

description: Replicate 3

value: Saline


title: MF_IV_2

description: Replicate 2


title: HER_IV_2

description: Replicate 2

value: Heroin


title: COC_VIII_2

description: Replicate 2

value: Cocaine


title: HER_I_2

description: Replicate 2


title: .SAL_VIII_2

description: Replicate 2


title: COC_II_2

description: Replicate 2


title: COC_I_2

description: Replicate 2


title: MF_VIII_1

description: Replicate 1

value: I


title: COC_IV_2

description: Replicate 2


title: NIC_I_3

description: Replicate 3

value: Nicotine


title: .SAL_I_2

description: Replicate 2


title: .SAL_IV_2

description: Replicate 2


title: .SAL_II_2

description: Replicate 2


title: MF_IV_1

description: Replicate 1


title: HER_VIII_2

description: Replicate 2


title: HER_VIII_1

description: Replicate 1


title: COC_IV_1

description: Replicate 1


title: .SAL_IV_1

description: Replicate 1


title: .SAL_VIII_1

description: Replicate 1


title: MF_II_1

description: Replicate 1


title: HER_II_1

description: Replicate 1


title: MF_I_1

description: Replicate 1


title: HER_IV_1

description: Replicate 1


title: COC_II_1

description: Replicate 1


title: HER_I_1

description: Replicate 1


title: COC_VIII_1

description: Replicate 1


title: COC_I_1

description: Replicate 1


title: .SAL_II_1

description: Replicate 1


title: .SAL_VIII_3

description: Replicate 3

value: III


title: .SAL_II_3

description: Replicate 3


title: .SAL_I_3

description: Replicate 3


title: .SAL_IV_3

description: Replicate 3


title: COC_II_3

description: Replicate 3


title: HER_I_3

description: Replicate 3


title: COC_VIII_3

description: Replicate 3


title: MF_VIII_3

description: Replicate 3


title: MF_IV_3

description: Replicate 3


title: MF_II_3

description: Replicate 3


title: COC_I_3

description: Replicate 3


title: HER_II_3

description: Replicate 3


title: HER_IV_3

description: Replicate 3


title: HER_VIII_3

description: Replicate 3


title: Small bowel juvenile polyps

status: Public on Apr 02 2010

type: genomic

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description: protocols according to manufacturer (Enzo Life Sciences or www.agilent.com)

hyb_protocol: Hybridization protocol available via www.agilent.com

scan_protocol: Slides were scanned using the Agilent microarray scanner, protocol according to Agilent.

data_processing: Smoothed log2 values(van de Wiel et al. Bioinformatics. 2009) of median signal intensity of green and red channel

molecule: genomic DNA

source_name: Small bowel juvenile polyps

label_protocol: DNA labeling protocol according to Enzo Life Sciences

extract_protocol: DNA isolation protocol available via www.vumc.nl/microarrays. Also described in Buffart et al, J Pathol. 2007 Jan;211(1):45-51

value: Small bowel juvenile polyps

source_name: male reference DNA

extract_protocol: DNAzol (Invitrogen) according to manufacturer's protocol

tag: reference

value: Pooled DNA from the blood of 18 normal individuals


title: MF_I_3

description: Replicate 3


title: Blood

source_name: Blood

value: Blood


title: Lung

source_name: Lung

value: Lung


title: Renal tumor D1

source_name: Renal tumor D1

value: Renal tumor

source_name: Pooled DNA from the blood of 18 normal individuals

value: male reference DNA


title: mut-vs-wt-rep2

status: Public on Mar 29 2010

city: Zurich

first: Valeria

last: Mozzetti

address: Schmelzbergstrasse 7

department: D-AGRL

country: Switzerland

institute: ETH

description: biological replicate mut-vs-wt

hyb_protocol: The hybridization conditions and the washing of the slide were performed as follows. To the 20 ul of cDNA (obtained with the Genisphere kit), 25 ul of control target Agilent, 60 ul of H2O and 105 ul of Agilent buffer were added. After 10 minutes of incubation at 80°C and 15 minutes at 65°C, the reaction was loaded on a pre-warmed slide in the hybridization chamber and incubated for 16 hours at 65°C, at four rpm in an Agilent oven. The cDNA hybridization was washed 10 min at 42°C in 6x SSC, 0.005% Triton x-100 and 10 min at RT in 0.2x SSC, 0.00016% Triton x-100. The 3DNA hybridization was carried out as described in the Genisphere protocol except for the hybridization volume which was increased to 204 ul and the washing modified as follows : 10 min at 65°C in 2x SSC, 0.0016% Triton x-100, 5 min at RT in 2x SSC, 0.0016% Triton x-100 and 10 min at RT in 0.2x SSC, 0.00016% Triton x-100.

scan_protocol: The slides were scanned at 10 um with a Scanarray 4000 (Packard Biochip Technologies, Billerica, MA, USA)

data_processing: Data were extracted with Imagene 5.6 (Biodiscovery, El Segundo, CA, USA). Data were treated with homemade scripts in Python language (www.python.org) and a local installation of the ArrayPipe web server (15). Probes showing a signal smaller than twice the standard deviation of the local background were considered without signal. Probes showing no signal or saturated signals in both channels were discarded from the analysis. Assuming an intensity-dependent variation in dye signal, (limma) loess global normalization was applied on signal ratios.

organism: Bifidobacterium longum

source_name: HPR2 mutant strain

label_protocol: RNA labelling and cDNA synthesis were carried out using the 3DNA Array 900 MPX Genisphere kit (Genisphere Inc., Hatfield, PA, USA) combined with the In situ Hybridization Kit Plus.

growth_protocol: in MRS cystein medium

extract_protocol: Total RNA extraction as described in Parche et al. 2006. J.Bacteriol. 188:1260-1265.

tag: genotype

value: mutant

source_name: NCC2705 wildtype strain

value: wildtype


title: mut-vs-wt-rep3

description: biological replicate mut-vs-wt


title: mut-vs-wt-rep1

description: biological replicate mut-vs-wt


title: Foreskin Melanocyte treated 10 hours with 1ug/ml of polyinosine-polycytidylic acid with polyethyleneimine

status: Public on Feb 01 2010

city: Madrid

first: Maria

middle: S

last: Soengas

address: Melchor Fernandez Almagro, 3

department: Molecular Pathology

country: Spain

institute: Spanish National Cancer Research Institute

description: no additional information

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Images were quantified using Agilent Feature Extraction Software

data_processing: Background substraction were carried out using normexp. Lowess method for within array normalization and quantiles method  for between array normalization were performed. Differentially expressed genes were obtained by using R limma package (Smyth et al., 2005) from Bioconductor project (http://www.bioconductor.org). Smyth GK, Michaud J and Scott HS. (2005). Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics 21: 2067-2075.

source_name: Foreskin Melanocyte Control 10h

label_protocol: Cy3 NT, Cy5 treated (pIC/PEI-pIC)

growth_protocol: Medium 254 supplemented with melanocyte growth factors (HMG-1) containing 10 ng/ml phorbol 12-myristate 13-acetateGrand Island, NY, USA) penicillin (100 U/ml), streptomycin (100 U/ml)

extract_protocol: Total RNA extracted using Qiagen Rneasy mini kit following manufacturer's instructions

treatment_protocol: control

value: Foreskin

tag: cell type

value: Melanocyte

tag: agent

value: control

tag: time

source_name: pIC+PEI treated Foreskin Melanocyte 10h

treatment_protocol: 1ug/ml of pIC or 1ug/ml pIC coupled with PEI

value: polyinosine-polycytidylic acid with polyethyleneimine (1ug/ml)


title: Renal tumor D2

source_name: Renal


title: Foreskin Melanocyte treated 10 hours with 1ug/ml of polyinosine-polycytidylic acid

description: no additional information

source_name: pIC treated Foreskin Melanocyte 10h

value: polyinosine-polycytidylic acid (1ug/ml)


title: Foreskin Melanocyte treated 4 hours with 1ug/ml of polyinosine-polycytidylic acid with polyethyleneimine

description: no additional information

source_name: Foreskin Melanocyte Control 4h

source_name: pIC+PEI treated Foreskin Melanocyte3 4h


title: DMSO_H2O1 with array type Medicago from Affymetrix

status: Public on Jan 01 2010

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

description: The involvement of ROS in the legume – Rhizobium symbiotic interaction has been highlighted (Santos et al., 2001; Rubio et al., 2004). This interaction is characterized by the formation of a new organ on the root, the nodule and by the penetration, in parallel, of the bacteria into the root tissue via an infection thread (IT) (Parniske and Downie, 2003; Gage, 2004). H2O2 production has been shown in ITs during the Medicago – Sinorhizobium meliloti interaction (Santos et al., 2001). Moreover, S. meliloti mutants impaired in H2O2 detoxification mechanism possess in planta symbiotic phenotypes. As H2O2 production is known to orchestrate plant gene expression, our goal is focused on identifying the H2O2 regulated genes in the symbiotic process. We focus our analysis in the M. truncatula transcriptome as we are characterising the S. meliloti H2O2 transcriptome.

hyb_protocol: labelled extract quantity: 15ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

label: Biotin

organism: Medicago truncatula

label_protocol: labelling Biotin direct, amplification=yes, cRNA 20 ug.

growth_protocol: root - Modified Fahraeus medium (in vitro), 25 degres, 16h, 80-100 µmol.m-2.s-1

treatment_protocol: Name:DMSO_H2O - compound based treatment - pathogen infection,dimethyl sulfoxide (dmso):time 72hour .

tag: harvest date

tag: cultivar

value: Jemalong


title: DPI_H2O2 with array type Medicago from Affymetrix

treatment_protocol: Name:DPI_H2O - compound based treatment - pathogen infection,diphenylene iodonium (dpi):quantity 10uM time 72hour .


title: DMSO_H2O2 with array type Medicago from Affymetrix


title: COC_IV_3

description: Replicate 3

source_name: Striatum of 6-10 week old C57BL/6J mice

value: Cocaine

value: X


title: DMSO_inoc2 with array type Medicago from Affymetrix

treatment_protocol: Name:DMSO_inoc - compound based treatment - pathogen infection,dimethyl sulfoxide (dmso):time 72hour .


title: Foreskin Melanocyte treated 4 hours with 1ug/ml of polyinosine-polycytidylic acid

description: no additional information

source_name: pIC treated Foreskin Melanocyte4h


title: DPI_inoc1 with array type Medicago from Affymetrix

treatment_protocol: Name:DPI_inoc - compound based treatment - pathogen infection,diphenylene iodonium (dpi):quantity 10uM time 72hour . µM


title: DPI_inoc2 with array type Medicago from Affymetrix


title: DMSO_inoc1 with array type Medicago from Affymetrix


title: Adult pancreas Frog replication 2

city: Baltimore

first: Donald

last: Brown

address: 3520 San Martin Dr

department: Department of Embryology

institute: Carnegie Institution

description: adult frog no T3 treatment

hyb_protocol: Agilent 60-mer oligo microarray processing protocol (SSC Wash/SureHyb Chamber set-up) V4.1, April 2004.  Agilent Publication Number:  G4140-90030 V4.1 APRIL 2004.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-64120) at 100% and 10% PMT in both channels, with a scan resolution of 5um.

data_processing:
Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.
The data is normalized with the following method:
(1) Take values from the columns gDyeNormSignal,rDyeNormSignal in the raw files and log-transform them using: log10(max(x,1)). These values will be referenced below as Xgi and Xri where i is array number.
(2) Take average of Xri's for the oligo among 16 arrays in the series:  AverXr = average(Xri).
(3) For each array estimate Yi = Xgi-Xri+AverXr
(4) Round Yi to 4 decimal digits. This is used as the normalized VALUE.
More detailed information with error correction can be found at http://lgsun.grc.nia.nih.gov/ANOVA/help.html#arrayjoin

organism: Xenopus laevis

source_name: Adult Frog, pancreas

label_protocol: Total RNA was labeled using Agilents Fluorescent Linear Amplification kit, according to manufacturers instructions (Product Number G2554A or P/N G2556-66002, Version 3.0, June 2002).

extract_protocol: TRIZOL standard extraction method was used . The full protocol can be found in the Life Technologies CAT 15596. Homogenize tissue samples in 1 mL of TRIZOL reagent per 50-100 mg of tissue using 1.5 Pellet Pestile (Nalge Nunc International). The sample volume should not exceed 10% of the volume of TRIZOL Reagent used for homogenization. Incubate the homogenized samples for 5 minutes at room temperature to permit the complete dissociation of nucleoprotein complexes. Add 0.2 mL of chloroform per 1 mL of TRIZOL Reagent. Cap sample tubes securely. Shake tubes vigorously by hand for 15 seconds and incubate them at room temperature for 2 to 3 minutes. Centrifuge the samples at no more than 12,000 x g for 15 minutes at 4 degree. Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. The volume of the aqueous phase is about 60% of the volume of TRIZOL Reagent used for homogenization. Transfer the aqueous phase to a fresh tube, and precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 mL of isopropyl alcohol per 1 mL of TRIZOL Reagent used for the initial homogenization. Incubate samples at room temperature for 10 minutes and centrifuge at no more than 12,000 x g for 10 minutes at 4 degree. The RNA precipitate, often invisible before centrifugation, forms a gel-like pellet on the side and bottom of the tube. Remove the supernate. Wash the RNA pellet once with 75% ethanol, adding at least 1 mL of 75% ethanol per 1 mL of TRIZOL Reagent used for the initial homogenization. Mix the sample by vortexing and centrifuge at no more than 7,500 x g for 5 minutes at 4 degree. Redissolving the RNA at the end of procedure, briefly drying the RNA pellet.

treatment_protocol: Adult mature frogs (females only) pancreas was dissected out.  Unlike tadpoles these frogs were not treated with either methimazole or thyroid hormone.  Pancreas was directly immersed in TRIZOL reagents for RNA extraction.

tag: development stage

value: adult

tag: gender

value: female

value: pancreas

value: untreated

tag: individual identifier

source_name: Universal RNA

extract_protocol: mRNAs were extracted with QuickPrep Micro mRNA Purification Kit from Amersham

value: Universal Xenopus Laevis Reference RNA


title: Adult pancreas Frog replication 1

description: adult frog no T3 treatment

tag: tissue


title: Adult pancreas Frog replication 3

description: adult frog no T3 treatment


title: Tadpole pancreas 48h replication 3

description: Stage 55, T3 exposure for 48 hours

source_name: Tadpole, pancreas, TH, 48h, NF55

treatment_protocol: Xenopus tadpoles (NF55) were treated with 1 mM methimazole in 0.1 X MMR  solution for 1 week to block the endogenous TH production and reduce the TH present in  the system of the tadpole. They were then treated with 100 nM T3 in 1 mM methimazole and 0.1 x MMR for another 48h. Samples were collected at 12h, 24h and 48h of exposure. Tadpoles exposed to 1mM MMI and not to T3 were control animals and they were collected at the time of last sampling of T3 exposure.  Tadpoles were euthanized with ice-cold MS222, excess water was blotted from the animals with tissue paper, small incision was made on the belly for quick fixation and samples were fixed in RNA-Later overnight at 4C and used for RNA extraction in TRIZOL reagent.  Pancreas from 5-10 tadpoles were pooled together as one replicate and there were three replicates at each time of exposure.

value: tadpole [Nieuwkoop and Faber stage (NF) 55]

value: Thyroid Hormone (TH)

value: 48 hours


title: HER_II_2

description: Replicate 2

tag: timepoint

value: Heroin

value: II


title: Tadpole pancreas Control replication 4

description: stage 55 control samples, No T3 Exposure

source_name: Tadpole, pancreas, Control


title: DPI_H2O1 with array type Medicago from Affymetrix


title: Tadpole pancreas 24h replication 3

description: Stage 55, T3 exposure for 24 hours

source_name: Tadpole, pancreas, TH, 24h, NF55

value: 24 hours


title: Tadpole pancreas 24h replication 2

description: Stage 55, T3 exposure for 24 hours


title: Tadpole pancreas 12h replication 3

description: Stage 55, T3 exposure for 12 hours

source_name: Tadpole, pancreas, TH, 12h, NF55

value: 12 hours


title: rib chondrocyte_cultured_WT

city: Setagaya

first: Hiroshi

last: Asahara

state: Tokyo

department: Department of Systems BioMedicine

country: Japan

institute: National Research Institute for Child Health and Development

description: Gene expression data from rib chondrocyte of Wt.

hyb_protocol: Hybridization to Affymetrix® GeneChip® Mouse Genome 430 2.0 arrays was carried out following standard Affymetrix® protocols.

scan_protocol: GeneChips® were scanned using GeneChip Scanner 3000

data_processing: Affymetrix® microarray image data were collected with Affymetrix® GeneChip® Command Console using default parameters. We used the Expression Console Version 1.1 software for data analysis. Signal intensities were calculated with the RMA using default parameters, including quantile normalization and log2 transformation.

source_name: rib chondrocyte,cultured,Wt

label_protocol: Biotinylated cRNA were prepared from total RNA following standard Affymetrix® protocols

extract_protocol: RNA of the culture was extracted using ISOGEN(NIPPONGENE).

tag: protocol

value: control

tag: strain

value: Strain:C57BL/6 ,CBA

tag: age

value: chondrocyte


title: Tadpole pancreas Control replication 2


title: Tadpole pancreas 48h replication 1

description: Stage 55, T3 exposure for 48 hours


title: Tadpole pancreas Control replication 3


title: Tadpole pancreas 12h replication 1

description: Stage 55, T3 exposure for 12 hours


title: rib chondrocyte_cultured_miR-140 KO

description: Gene expression data from rib chondrocyte of miR-140 KO.

source_name: rib chondrocyte,cultured,miR-140 KO

value: microRNA-140 depletion


title: Tadpole pancreas 24h replication 1

description: Stage 55, T3 exposure for 24 hours


title: Tadpole pancreas Control replication 1


title: Tadpole pancreas 48h replication 2

description: Stage 55, T3 exposure for 48 hours


title: Tadpole pancreas 62-Pan#1

data_processing:
Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.
The data is normalized with the following method:
(1) Take values from the columns gDyeNormSignal,rDyeNormSignal in the raw files and log-transform them using: log10(max(x,1)). These values will be referenced below as Xgi and Xri where i is array number.
(2) Take average of Xri's for the oligo among 9 arrays in the series:  AverXr = average(Xri).
(3) For each array estimate Yi = Xgi-Xri+AverXr
(4) Round Yi to 4 decimal digits. This is used as the normalized VALUE.
More detailed information with error correction can be found at http://lgsun.grc.nia.nih.gov/ANOVA/help.html#arrayjoin

source_name: Tadpole, pancreas, NF62

treatment_protocol: Xenopus tadpoles (NF52, NF62, and NF66) were euthanized with ice-cold MS222, excess water was blotted from the animals with tissue paper, small incision was made on the belly for quick fixation and samples were fixed in RNA-Later overnight at 4C and used for RNA extraction in TRIZOL reagent.  Pancreas and liver from 5-10 tadpoles were pooled together as one replicate and there were three replicates at each time of exposure.

value: tadpole [Nieuwkoop and Faber stage (NF) 62]


title: Tadpole liver 66-Li  #3

source_name: Tadpole, liver, NF66

value: tadpole [Nieuwkoop and Faber stage (NF) 66]

value: liver


title: Tadpole pancreas 66-Pan#1

source_name: Tadpole, pancreas, NF66

value: pancreas


title: Tadpole pancreas 62-Pan#3


title: Tadpole pancreas 66-Pan#2


title: Tadpole pancreas 12h replication 2

description: Stage 55, T3 exposure for 12 hours


title: Tadpole pancreas 66-Pan#3


title: Tadpole pancreas 52-Pan#2

source_name: Tadpole, pancreas, NF52

value: tadpole [Nieuwkoop and Faber stage (NF) 52]


title: Tadpole pancreas 52-Pan#1

value: Universal Xenopus Laevis Reference RNA


title: Tadpole liver 62-Li #3

source_name: Tadpole, liver, NF62


title: Tadpole pancreas 52-Pan#3


title: Tadpole liver 66-Li  #2


title: Tadpole pancreas 62-Pan#2


title: Tadpole liver 62-Li #1


title: Tadpole liver 62-Li #2


title: Tadpole liver 66-Li  #1


title: .SAL_I_1

description: Replicate 1

tag: drug

value: Saline

tag: group no.

tag: large batch

value: X

tag: plate

value: I


title: Tadpole liver 52-Li #3

source_name: Tadpole, liver, NF52

value: Thyroid Hormone (TH)

tag: reference


title: Tadpole liver 52-Li #2

tag: agent


title: Tadpole liver 52-Li #1


title: Epithelioid_6

status: Public on Dec 31 2009

city: Nagoya

first: Shinya

last: Toyokuni

state: Aichi

address: 65 Tsuruma-Cho, Showa-Ku

institute: Nagoya University

description: Original sample number: FB15-5

hyb_protocol: According to the manufacturer’s protocol (One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling), Version 5.7, March 2008).

scan_protocol: According to the manufacturer’s protocol (One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling), Version 5.7, March 2008, Agilent Scanner Settings).

data_processing:
Microarray data were analyzed following import into GeneSpring GX 10.0.2 software (Agilent Technologies)
Threshold: 1.0
Logbase: 2
Technology: Agilent.SingleColor.14879
Normalization: Shift to 75 percentile
Baseline Transformation: Median of Control Samples

organism: Rattus norvegicus

source_name: F1 from Fischer344 and Brown-Norway, male, ferric saccharate induced mesothlioma of epithelioid types

extract_protocol: RNA was extracted using RNeasy Mini(QIAGEN).

treatment_protocol: ferric saccharate induced

value: F1 from Fischer344 and Brown-Norway

value: male

value: mesothlioma of epithelioid types

tag: sample

value: tumor


title: Control_peri-testicular_1

description: Original sample number: tes_1

source_name: Peri-testicular tissue of 8 week male rat untreated

label_protocol: According to the manufacturer’s protocol (One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling), Version 5.7, March 2008).

value: Fischer 344

value: control

value: Peri-testicular tissue


title: Epithelioid_3

description: Original sample number: FB15-1


title: Sarcomatoid_1

description: Original sample number: FB10-4

source_name: F1 from Fischer344 and Brown-Norway, male, ferric saccharate induced mesothlioma of sarcomatoid types

value: mesothlioma of sarcomatoid types


title: Epithelioid_4

description: Original sample number: FB15-2


title: NS5_4

city: London

first: Caroline

middle: Emma

last: Johnston

address: 125 Coldharbour Lane

country: United Kingdom

institute: Kings College London

hyb_protocol: Amplified RNA were hypridised on Sentrix Mouse Ref-8 (v1.1) Expression BeadChips (Illumina, USA, Cat# 11234312) according to Illumina protocols

scan_protocol: Chips were washed and scanned according to Illumina protocols

data_processing: Quantile normalisation, log2 transformation using the beadarray Bioconductor library in R

source_name: NS5 Neural Stem Cells

label_protocol: 4 biological replicates of total RNA extracted from each of NS5 and Astrocyte cells were subjected to reverse transcription, second-strand cDNA synthesis and in vitro transcription using Illumina TotalPrep RNA Amplification Kit (Ambion, USA, Cat# IL1791).   Biotin was incorporated into amplified RNA through use of biotin-modified dUTP.

growth_protocol: NS5 cells were grown as described in Conti et al, PLoS Biology Vol. 3, No. 9, e283 doi:10.1371/journal.pbio.0030283

extract_protocol: Cells were detached from tissue culture plates, pelleted and lysed with TRIzol reagent (Invitrogen, Cat# 15596-018) as per kit instruction. The resultant total RNA extracts were further cleaned up with Qiagen RNEasy Mini Kit (Qiagen Cat# 74106) as per kit instruction

treatment_protocol: For differentiation into GFAP-positive cells, NS5s were seeded at 5x104 cells/cm2 in normal growth medium (NGM) on gelatin-coated plastic or glass coverslips overnight before medium was switched into NGM in the absence of growth factors and with the addition of 5% FCS for 3 days. Cells were routinely passaged with a 1:5-10 split using trypsin/EDTA

tag: cell line


title: Epithelioid_1

description: Original sample number: FB1-1


title: Drn1/WT-3

city: Aurora

first: Jay

middle: R.

last: Hesselberth

state: CO

department: Biochemistry and Molecular Gentetics

institute: University of Colorado School of Medicine

description: Biological replicate #2

hyb_protocol: Agilent standard protocol

scan_protocol: Agilent standard protocol

data_processing: Data processed using marray package from Bioconductor.

label: Alexa Fluor 532

organism: Saccharomyces cerevisiae

source_name: Log-phase cells

label_protocol: Total RNA labeled using Ulysis Direct RNA labeling kit (Invitrogen)

growth_protocol: Yeast grown in YPD at 30 C to log-phase

extract_protocol: Total RNA isolated using acid phenol

treatment_protocol: No treatment

label: Alexa Fluor 647

value: BY4743 drn1∆


title: Sarcomatoid_2

description: Original sample number: FB12-4

value: female


title: Astrocyte_3

source_name: Neural Stem Cell-Derived Astrocytes


title: Drn1/WT-2

description: Biological replicate #1 - dye swap


title: Control_methoserial_2

description: Original sample number: mes_2

source_name: Scraped pleural mesothelial cells of 8 week male rat untreated

value: Scraped pleural mesothelial cells


title: Drn1/WT-4

description: Biological replicate #2 - dye swap


title: Control_peri-testicular_2

description: Original sample number: tes_2


title: NS5_3


title: Epithelioid_5

description: Original sample number: FB15-4


title: Astrocyte_2


title: Astrocyte_4


title: Epithelioid_2

description: Original sample number: FB13-2


title: NS5_1


title: NS5_2


title: sow 2-6 mm, biological rep3

city: Urbana

first: Rebecca

last: Krisher

state: IL

address: 1207 West Gregory Drive

institute: University of Illinois

description: Gene expression data of developmentally competent (adult) derived oocytes

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

molecule: polyA RNA

organism: Sus scrofa

source_name: sow derived oocytes at metaphase II collected from 2-6 mm follicles

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol following two-cycle amplification.

growth_protocol: Oocytes were matured in vitro for 42-44 hours in modified Tissue Culture Medium 199.

extract_protocol: Poly A+ RNA extraction was performed using the DynaBeads mRNA Direct Kit from Invitrogen.

treatment_protocol: After in vitro maturation, oocytes were exposed to 1% v/v (80-160 U/mL) hyaluronidase and vortexed for 6-8 minutes to remove the cumulus cells.  Oocytes were examined for the presence of the first extruded polar body in SOF-Hepes supplemented with 5% sucrose to shrink the ooplasm.

tag: Age

value: adult

tag: Follicle Size


title: gilt 2-6 mm, biological rep2

description: Gene expression data of developmentally incompetent (prepubertal) derived oocytes

source_name: gilt derived oocytes at metaphase II collected from 2-6 mm follicles

value: prepubertal


title: Control_methoserial_1

description: Original sample number: mes_1


title: Drn1/WT-1

description: Biological replicate #1


title: sow 2-6 mm, biological rep1


title: pre induction larvae vs LWamide induced larvae 12h post induction

status: Public on Dec 07 2009

city: Canberra

first: Lauretta

last: Grasso

state: ACT

address: Biology Place

department: Research School of Biological Sciences

country: Australia

institute: Australian National University

description: Both samples were labeled with Cy3 and hybridised separately with a Cy5 labeled common reference sample. The Cy5 labeled common reference was a pool of equal parts of all of the test samples. For hybridisation, the same quantity of RNA as used for the test sample was Cy5 labeled for co-hybridisation with the Cy3 labeled sample.

scan_protocol: The slides were scanned using a GenePix 4200 scanner.  The data were extracted with Spot (CSIRO).

data_processing: All analyses were done using the limma package {Smyth, 2005 #152} for the R system (http://www.r-project.org/).  ‘Normexp’ background correction (Ritchie et al 2007) and print-tip loess normalisation {Smyth, 2003 #150} was performed on each slide, in order to account for intensity-dependent dye bias.  The methodology used for statistical analysis is described in Smyth {Smyth, 2004 #151}.  The prior probability of differential expression, for each pair of comparisons between stages, was taken as 0.1.  The Benjamini and Hochberg method (2001) was used to adjust the sequence-wise p-values, so that a choice of sequences for which the adjusted p-value is at most 0.05 identifies a set of differentially expressed genes in which 5% may be falsely identified as differentially expressed.

label: Cy3, Cy5

organism: Acropora millepora

source_name: pre induction larvae; common reference

label_protocol: As per instructions of the manufacturer of the Superscript Indirect RNA Amplification System (Invitrogen)

tag: pre induction

source_name: LWamide induced larvae, 12h post induction; common reference

tag: 12h post induction


title: gilt 2-6 mm, biological rep3


title: Astrocyte_1


title: pre induction larvae vs crustose coralline algae extract induced larvae 12h post induction

extract_protocol: As per instructions of the manufacturer of the Superscript Indirect RNA Amplification System (Invitrogen)

source_name: crustose coralline algae extract induced larvae, 12h post induction; common reference


title: pre induction larvae vs crustose coralline algae induced larvae 12h post induction

source_name: crustose coralline algae induced larvae, 12h post induction; common reference


title: pre induction larvae vs crustose coralline algae extract induced larvae 4h post induction

source_name: crustose coralline algae extract induced larvae, 4h post induction; common reference

tag: 4h post induction


title: pre indcution larvae vs crustose coralline algae induced larvae 4h post induction

tag: pre induction larvae

source_name: crustose coralline algae induced larvae, 4h post induction; common reference


title: pre induction larvae vs LWamide induced larvae 4h post induction

source_name: LWamide induced larvae, 4h post induction; common reference


title: pre induction larvae vs control larvae 0.5h after induction of test samples

source_name: control larvae, 0.5h post induction of test samples; common reference

tag: 0.5h post induction of test samples


title: sow 2-6 mm, biological rep2


title: pre induction larvae vs control larvae 4h post induction of test samples

source_name: control larvae, 4h post induction of test samples; common reference

tag: 4h post induction of test samples


title: gilt 2-6 mm, biological rep1


title: pre induction larvae vs control larvae 12h post induction of test samples

source_name: control larvae, 12h post induction of test samples; common reference

tag: 12h post induction of test samples


title: LWamide induced larvae 0.5h vs 4h post indcution

source_name: LWamide induced larvae, 0.5h post induction; common reference

tag: 0.5h post induction


title: crustose coralline algae extract induced larvae 0.5h vs 4h post induction

source_name: crustose coralline algae extract induced larvae, 0.5h post induction; common reference


title: pre induction larvae vs LWamide induced larvae 0.5h post induction


title: control larvae 0.5 vs 4h post induction


title: pre induction larvae vs crustose coralline algae induced larvae 0.5h post induction

source_name: crustose coralline algae induced larve, 0.5h post induction; common reference


title: control larvae 4h vs 12h post induction

source_name: control larvae, 4h post induction; common reference

source_name: control larvae, 12h post induction; common reference


title: LWamide induced larvae 4h vs 12h post induction


title: crustose coralline extract induced larvae 4h vs 12h post induction

source_name: crustose coralline extract induced larvae, 4h post induction; common reference

source_name: crustose coralline extract induced larvae, 12h post induction; common reference


title: crustose coralline algae induced larvae 0.5h vs 4h post induction

source_name: crustose coralline algae induced larvae, 0.5 hours post induction; common reference

tag: 0.5 hours post induction

source_name: crustose coralline algae induced larvae, 4 hours post induction; common reference

tag: 4 hours post induction


title: R. amphibia genomic DNA

status: Public on Dec 01 2009

first: Alex

last: Boonman

address: Kruislaan 318

department: IBED

institute: Universiteit van Amsterdam

description: R. amphibia genomic DNA used to make a probe mask. Genomic DNA was extracted using the Qiagen DNeasy Plant Mini Kit. 500 ng DNA was amplified and labeled using the Bioprime DNA labelling kit (Invitrogen) and 6.1 ug DNA was hybridised to the Affymetrix Ath1 Arabidopsis GeneChip

hyb_protocol: 6.1 ug DNA was hybridised to the Affymetrix Ath1 Arabidopsis GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 7G.

data_processing: The data were analyzed with Genespring GX using the Robust Multichip Average (RMA) algorith and quantile normalization. A probe mask was applied based on the genomic DNA hybridisations and using a genomic DNA hybridisation intensity threshold of 80

organism: Rorippa amphibia

source_name: R. amphibia genomic DNA

label_protocol: 500 ng DNA was amplified and labeled using the Bioprime DNA labelling kit (Invitrogen). Nanodrop and Bioanalyzer evaluation was used.

growth_protocol: Rhizomes of each genotype were surface sterilized, cut into pieces and placed on agar medium in a light cabinet for 11 days for sprouts to develop. Individual meristems were excised and placed on pots filled with sand and supplemented with complete nutrient solution in a greenhouse. Plants were grown under natural daylight in the greenhouse for a further three weeks until the start of treatment

extract_protocol: Genomic DNA was extracted using the Qiagen DNeasy Plant Mini Kit. Nanodrop and Bioanalyzer evaluation was used.

treatment_protocol: Control plants were placed individually in opaque 16 liter plastic bucketsin the greenhouse and submerged plants were placed in the same buckets filled with rain water. Treatment started at noon and lasted 24 hours. No supplemental lighting was given, water was not stirred or replaced, plants were completely submerged during the treatment. Individuals were randomly assigned to either the control or submerged condition and to a position in the greenhouse.

tag: clonal plant origin

value: Clonal plants derived from a R. amphibia rhizome collected along the Yssel river near Doesburg, the Netherlands (N:52º01'25'' E:06º08'42'') and a R. sylvestris rhizome was collected along the river Rhine near Millingerwaard, the Netherlands (N:51º52'02'' E:06º08'42'')


title: crustose coralline algae induced larvae 4h vs 12h post induction

source_name: crustose coralline algae induced larvae, 12 hours post induction; common reference

tag: 12 hours post induction


title: F1 hybrid, submerged, rep2

description: gene expression data from roots of 24h submerged F1 hybrid roots after applying a probe mask with genomic DNA hybridisation intensity threshold 80

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Ath1 Arabidopsis GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

organism: Rorippa anceps

source_name: F1 hybrid, submerged, roots

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was extracted from frozen, homogenized material using the Qiagen RNeasy Plant Mini kit according to the manufacturer's instructions

value: Clonal plants derived from one germinated seed of an interspecific cross between the Rorippa amphibia and Rorippa sylvestris genotypes described here


title: R. sylvestris, submerged, rep3

description: gene expression data from roots of 24h submerged R. sylvestris roots after applying a probe mask with genomic DNA hybridisation intensity threshold 80

organism: Rorippa sylvestris

source_name: R. sylvestris, submerged, roots

value: Clonal plants derived from a R. sylvestris rhizome collected along the river Rhine near Millingerwaard, the Netherlands (N:51º52'02'' E:06º08'42'')


title: R. sylvestris, submerged, rep1


title: R. amphibia, submerged, rep1

description: gene expression data from roots of 24 h submerged R. amphibia roots after applying a probe mask with genomic DNA hybridisation intensity threshold 80

source_name: R. amphibia, submerged, roots


title: R. sylvestris, submerged, rep2


title: R. sylvestris, air, rep1

description: gene expression data from roots of air controls of R. sylvestris roots after applying a probe mask with genomic DNA hybridisation intensity threshold 80

source_name: R. sylvestris, air, roots


title: R. amphibia, submerged, rep2


title: R. amphibia, air, rep3

description: gene expression data from roots of air controls of R. amphibia roots after applying a probe mask with genomic DNA hybridisation intensity threshold 80

source_name: R. amphibia, air, roots


title: F1 hybrid, air, rep3

description: gene expression data from roots of air controls of F1 hybrid roots after applying a probe mask with genomic DNA hybridisation intensity threshold 80

source_name: F1 hybrid, air, roots


title: F1 hybrid, air, rep2


title: R. amphibia, submerged, rep3


title: R. sylvestris, air, rep2


title: R. sylvestris genomic DNA

description: R. sylvestris genomic DNA used to make a probe mask. Genomic DNA was extracted using the Qiagen DNeasy Plant Mini Kit. 500 ng DNA was amplified and labeled using the Bioprime DNA labelling kit (Invitrogen) and 6.1 ug DNA was hybridised to the Affymetrix Ath1 Arabidopsis GeneChip

source_name: R. sylvestris genomic DNA


title: F1 hybrid, air, rep1


title: R. amphibia, air, rep2

value: clonal plants derived from a r. amphibia rhizome collected along the yssel river near doesburg, the netherlands (n:52º01'25'' E:06º08'42'') and a R. sylvestris rhizome was collected along the river Rhine near Millingerwaard, the Netherlands (N:51º52'02'' E:06º08'42'')


title: R. amphibia, air, rep1


title: F1 hybrid, submerged, rep1


title: F1 hybrid, submerged, rep3


title: R. sylvestris, air, rep3


title: Aortic valve Eln+/- AV_TG_2

status: Public on Nov 30 2009

city: Cincinnati

first: Robert

middle: Bruce

last: Hinton

state: OH

address: 3333 Burnet Ave

department: Dept Of Pediatrics

institute: Cincinnati Children's Hospital Medical Center

description: Aortic valve tissue (consisting of cusp, annulus and root) and ascending aorta tissue was obtained from both Eln+/+ and Eln+/- mice (total 16 experiments).

hyb_protocol: Full Protocol Description: Use a standard Probe Array Cartridge (GeneChip Mouse Genome 430 2.0 Array– Affymetrix). Create a hybridization cocktail for a single probe array that contains 5 mg of fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 10% DMSO, and 1X Hybridization Buffer.  Heat hybridization cocktail to 99°C for 2 minutes, to 45°C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 mL of 1X Hybridization Buffer. Incubate at 45°C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 mL of the hybridization cocktail. Incubate at 45°C for 18 hrs in the Hybridization Oven rotating at 60 rpm. Fluidics:  Wash and Stain probe arrays using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0004. Arrays were stained with phycoerythrin-conjugated streptavidin [Molecular Probes, Eugene, OR] and hybridization signals were amplified using antibody amplification with anti-streptavidin biotinylated antibody [Vector Laboratories, Burlingame, CA], as described in the Affymetrix GeneChip® Expression Analysis Manual.

scan_protocol: Images were scanned using a Genechip scanner 3000 [Affymetrix]

data_processing:
Affymetrix Gene Chip Mouse Genome 430 2.0 array gene chips were used.  Gene Chip CEL files were subjected to RMA normalization using GeneSpring GX 7.3 software [Agilent].  Each gene was normalized to the median value of that gene.
Standard Affymetrix internal control genes were used to check the quality of the assay quality by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and B-actin, with acceptable 3' to 5' ratios between1-3. Prokaryotic Spike controls were used to determine the hybridization of target RNA to the array occurred properly.
GeneSpring 7.3 (Agilent Technologies Inc. Palo Alto, California) was used for normalization and filtering. Data were analyzed using Ingenuity Pathway Analysis (Ingenuity® Systems, www.ingenuity.com). Fisher’s exact test was used to calculate a p-value determining the probability that the association between the genes in the dataset and the canonical pathway is explained by chance alone.

source_name: Postnatal day 30 Eln+/+ aorta, postnatal day 30 Eln+/- aorta; postnatal day 30 Eln+/+ aortic valve; postnatal day 30 Eln+/- aortic valve

label_protocol: 1-20 ng of total RNA from each tissue specimen from each animal was used in an independent experiment (there was no tissue pooling). Use the WT- Ovation Pico RNA Amplification System Version 1.0 (Nugen) to prepare target cDNA. Then use the FL-Ovation cDNA Biotin Module V2 (Nugen) to fragment and biotin label the target cDNA.

extract_protocol:
Heart tissue was dissected from 30 day old Eln+/+ and Eln+/- mice, and aortic valve and ascending aorta tissue was isolated and immediately submerged in Trizol [Invitrogen].
The quality of the Total RNA is checked by the Agilent Bioanalyzer 2100 (Hewelett Packard) using the RNA 6000 Pico Assay.

tag: tissue

value: aortic valve

tag: genotype

value: Elastin +/-

tag: age

value: 30 days


title: Aortic valve Eln+/+ AV_WT_2

value: Elastin +/+


title: Aortic valve Eln+/+ AV_WT_4


title: Aortic valve Eln+/- AV_TG_3


title: Aortic valve Eln+/+ AV_WT_1


title: Aortic valve Eln+/- AV_TG_1


title: Aorta Eln+/- AO_TG_4

value: aorta


title: Aortic valve Eln+/+ AV_WT_3


title: LFSO_group4-2

status: Public on Nov 29 2009

city: St Genes-Champanelle

first: Christine

last: Leroux

address: Centre INRA de Theix

department: PHASE

description: The signal and background median intensities for the Cy3 and Cy5 channels from each spot were obtained using ImaGene 6.0 software (BioDiscovery, Inc).

hyb_protocol: 40 pmol of Cy3-labeled cDNA and 40 pmol of Cy5-labeled cDNA were co-hybridized at 42°C for 16 h on the oligoarray “URH-TALL _Bovine_Operon V1.1_2”. The pre-hybridization treatments, hybridization and washes were performed using the Pronto Plus Direct System (Promega and Corning B.V. Life Sciences) according to the manufacturer’s instructions.

scan_protocol: The slide was scanned for both dye channels at 532 and 635 nm with an InnoScan 700A scanner (Innopsys) at 10 µm resolution.

data_processing: Low-expressed and missing spots (spots with a background mean-subtracted signal mean < 3 background SD), poor-quality spots, and saturated spots were filtered before normalization. After a base-2 logarithm transformation, data were normalized by a global Lowess regression followed by a block effect correction via the subtraction of the median by block using R2.6 software (http://www.r-project.org).

organism: Capra hircus

label_protocol: 5 µg of pooled total RNA sample were labeled with Cy5-dCTP (Amersham Biosciences Europe Gmbh) using the Pronto Plus Direct System (Promega and Corning B.V. Life Sciences) according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted using the SV Total RNA Isolation system (Promega), including a DNase treatment step. RNA concentration and purity were determined by spectrophotometry at 260, 280 and 320 nm and RNA integrity was verified using a Bioanalyser 2100 (Agilent Technologies).

tag: Tissue

value: lactating mammary gland,

tag: Pooled sample

value: equal amounts (1.25 µg) of total RNA sample from mammary gland of each goat belonging to the same Latin Square group were mixed together before labeling,

tag: Goats no.

tag: Treatment

value: low forage with 130 g/d of sunflower oil

label_protocol: 5 µg of reference total RNA were labeled with Cy3-dCTP (Amersham Biosciences Europe Gmbh) using the Pronto Plus Direct System (Promega and Corning B.V. Life Sciences) according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted using a method derived from Chomczynski and Sacchi and further purified with the SV Total RNA Isolation System (Promega). RNA concentration and purity were determined by spectrophotometry at 260, 280 and 320 nm and RNA integrity was verified using a Bioanalyser 2100 (Agilent Technologies).

tag: Reference

value: pool of caprine lactating mammary gland, muscle, adipose tissue, heart, liver, spleen, kidney, lung, and uterus


title: LFSO_group1-1

label_protocol: 5 µg of pooled total RNA sample were labeled with Cy3-dCTP (Amersham Biosciences Europe Gmbh) using the Pronto Plus Direct System (Promega and Corning B.V. Life Sciences) according to the manufacturer’s instructions.

label_protocol: 5 µg of reference total RNA were labeled with Cy5-dCTP (Amersham Biosciences Europe Gmbh) using the Pronto Plus Direct System (Promega and Corning B.V. Life Sciences) according to the manufacturer’s instructions.


title: LFSO_group3-2


title: Aorta Eln+/- AO_TG_1


title: Aorta Eln+/+ AO_WT_1


title: LFSO_group3-1


title: Aorta Eln+/+ AO_WT_2


title: LFSO_group2-2


title: Aorta Eln+/+ AO_WT_3


title: LF_group4-1

value: low forage (43:57 forage to concentrate ratio)


title: LF_group3-2


title: Aorta Eln+/- AO_TG_2


title: LFSO_group2-1


title: LF_group4-2


title: LFSO_group1-2


title: LFSO_group4-1


title: LF_group2-2


title: Aorta Eln+/- AO_TG_3


title: LF_group1-1


title: HFRS_group3-1

value: high forage with 460 g/d of whole rapeseeds


title: HFRS_group3-2


title: LF_group2-1


title: HFRS_group4-1


title: LF_group1-2


title: HFRS_group4-2


title: Aortic valve Eln+/- AV_TG_4


title: HFRS_group2-2


title: HFRS_group2-1


title: HF_group2-1

value: high forage (64:36 forage to concentrate ratio)


title: HFRS_group1-1


title: HF_group1-2


title: HF_group4-1


title: HFRS_group1-2


title: HF_group4-2


title: HF_group3-2


title: HF_group2-2


title: LF_group3-1


title: HF_group3-1


title: H929-Lovastatin-rep3

status: Public on Nov 24 2009

city: Toronto

first: Paul

middle: C

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

hyb_protocol: The IVT products were then column-purified, fragmented, and hybridized onto Affymetrix Human U133 Plus 2.0 GeneChips® at 45º C for 16 h.

scan_protocol: Subsequent to hybridization, the arrays were washed and stained with streptavidin-phycoerythrin, then scanned in an Affymetrix GeneChip® Scanner 3000 (Santa Clara, CA).  All control parameters were confirmed to be within normal ranges before normalization and data reduction was initiated.

data_processing: Data was loaded into the R statistical environment (v2.7.2) using the affy package (v1.18.2) of the BioConductor open-source library. All arrays appeared robust, with minimal distributional or spatial heterogeneity; none were excluded. Data was pre-processed using the gcrma algorithm, as implemented in the gcrma package of BioConductor (v2.12.1). A custom CDF (hgu133plus2hsentrezgcdf) was used to provide an updated and one-to-one mapping of ProbeSets to Entrez Gene IDs (v11.0.0).

source_name: H929 cells, lovastatin treated

label_protocol: Array protocols were conducted according to manufacturer's instructions for the Affymetrix One Cycle Target Labeling and Control Reagents kit (Santa Clara, CA).  Briefly, cDNA was generated from 1 µg of total RNA using SuperScript II reverse transcriptase (Invitrogen, Carlsbad, CA) and T7 Oligo(dT) primer.  Subsequently, the products were column-purified (Affymetrix) and then in vitro transcribed to generate biotin-labeled cRNA.

growth_protocol: Cells were seeded sub-confluently overnight in RPMI 1640 +10% FBS +antibiotics

extract_protocol: Cells were pelleted and then lysed in TRIZOL reagent as per manufacturer's instructions.  Briefly, cell pellets were resuspended in 1mL of TRIZOL reagent and lysed by repetitive pipetting.  Phase separation with chloroform, RNA precipitation, and RNA washes were carried out as described and the RNA pellets were dissolved in RNase-free water.  RNA was then purified with a Qiagen RNeasy micro kit.

treatment_protocol: Cells were exposed to 20uM lovastatin or ethanol vehicle control for 16 hours

tag: cell line

tag: cell type

value: multiple myeloma

value: statin sensitive

tag: treatment

value: lovastatin


title: KMS11-Ethanol-rep3

source_name: KMS11 cells, ethanol treated

value: ethanol


title: H929-Ethanol-rep3

source_name: H929 cells, ethanol treated


title: SKMM1-Ethanol-rep2

source_name: SKMM1 cells, ethanol treated

value: statin insensitive


title: SKMM1-Lovastatin-rep2

source_name: SKMM1 cells, lovastatin treated


title: SKMM1-Lovastatin-rep3


title: LP1-Lovastatin-rep2

source_name: LP1 cells, lovastatin treated


title: KMS11-Lovastatin-rep3

source_name: KMS11 cells, lovastatin treated


title: SKMM1-Ethanol-rep3


title: LP1-Ethanol-rep3

source_name: LP1 cells, ethanol treated


title: LP1-Lovastatin-rep3


title: LP1-Ethanol-rep2


title: H929-Ethanol-rep2


title: HF_group1-1


title: H929-Lovastatin-rep2


title: Ho998 1h 2

status: Public on Nov 16 2009

city: Berne 9

first: Martin

last: Flück

state: Bern

address: Bühlstrase 26

department: Department of Anatomy

institute: University of Berne

description: Samples corresponding to different time-points of recovery from exercise of one individual before or after training, respectively, were analyzed in parallel.

hyb_protocol: Equal amounts (1-3 Mio cpm) of cDNA target were hybridized to individual cDNA array filters in Expresshyp (BD Biosciences, Allschwil, Switzerland) at 68ºC o/n

scan_protocol: Filters were washed and exposed to a phosphor imager for 10 days (Molecular Dynamics, Sunnyvale, USA).

data_processing: Expression was quantified from raw signal intensities in relation to the background as estimated using the Grid Background Dots mode for 54 selected dots (AIDA Array Easy software, Raytest, Urdorf, Switzerland).

source_name: vastus lateralis muscle

label_protocol: Standardized amounts of [alpha-32P-dCTP] were used per reaction. Radiolabelled cDNA target was purified from the reaction using the supplied cartridge (BD Biosciences).

extract_protocol:
total RNA was isolated from 25 micrometer cryosections of the muscle biopsies using RNeasy kit (Qiagen).
2.5 micogram total RNA was reverse-transcribed using Superscript II (Invitrogen, Basel, Switzerland).

treatment_protocol:
The sample was collected with a needle biopsy.
Samples were snap frozen in liquid nitrogen-cooled isopentane and kept frozen at -70 deg C.

tag: time of biopsy

value: after 1 hour of recovery after cessation of a 30 minutes single bout of endurance exercise at simulated altitude of 4000m in the trained state.


title: Ho996 8h 1

value: after 8 hours of recovery after cessation of a 30 minutes single bout of endurance exercise at simulated altitude of 4000m in the untrained state.


title: Ho996 24h 1

label_protocol: 2.5 micogram total RNA was reverse-transcribed using Superscript II (Invitrogen, Basel, Switzerland). Standardized amounts of [alpha-32P-dCTP] were used per reaction. Radiolabelled cDNA target was purified from the reaction using the supplied cartridge (BD Biosciences).

extract_protocol: total RNA was isolated from 25 micrometer cryosections of the muscle biopsies using RNeasy kit (Qiagen).

value: after 24 hours of recovery after cessation of a 30 minutes single bout of endurance exercise at simulated altitude of 4000m in the untrained state.


title: SKMM1-Lovastatin-rep1


title: Ho998 8h 2

value: after 8 hours of recovery after cessation of a 30 minutes single bout of endurance exercise at simulated altitude of 4000m in the trained state.


title: Ho998 24h 2

value: after 24 hours of recovery after cessation of a 30 minutes single bout of endurance exercise at simulated altitude of 4000m in the trained state.


title: LP1-Ethanol-rep1


title: Ho998 24h 1


title: H929-Lovastatin-rep1


title: Ho996 pre 1

treatment_protocol:
Resting biopsies were taken from the vastus lateralis muscle using the Bergstroem technique.
Tissue was snap frozen in liquid nitrogen-cooled isopentane and kept frozen at -70 deg C.

value: Resting biopsy before 30 minutes of endurance exercise in the untrained state.


title: LP1-Lovastatin-rep1


title: Ho994 24h 2


title: Ho998 pre 2

value: Resting biopsy before 30 minutes of endurance exercise in the trained state.


title: KMS11-Lovastatin-rep2


title: Ho998 1h 1

value: after 1 hour of recovery after cessation of a 30 minutes single bout of endurance exercise at simulated altitude of 4000m in the untrained state.


title: Ho994 1h 2


title: H929-Ethanol-rep1


title: Ho994 8h 2


title: Ho998 8h 1


title: Ho994 pre 2


title: KMS11-Ethanol-rep1


title: KMS11-Lovastatin-rep1


title: SKMM1-Ethanol-rep1


title: Ho996 1h 1


title: Ho994 24h 1


title: Ho994 8h 1


title: Ho998 pre 1


title: Ho984 8h 1


title: Ho984 8h 2


title: Ho984 pre 1


title: Ho984 1h 2


title: Ho994 1h 1


title: Ho994 pre 1


title: Ho984 1h 1


title: Ho982 8h 2

hyb_protocol: Equal amounts (1-3 Mio cpm) of cDNA target were hybridized to individual cDNA array filters in Expresshyp (BD Biosciences, Allschwil, Switzerland) at 68ºC o/n.

growth_protocol:
Resting biopsies were taken from the vastus lateralis muscle using the Bergstroem technique.
Tissue was snap frozen in liquid nitrogen-cooled isopentane and kept frozen at -70 deg C.


title: Ho984 24h 1


title: Ho982 24h 1


title: Ho982 8h 1


title: Ho982 24h 2


title: Ho982 pre 2


title: Ho982 pre 1

treatment_protocol:
Resting needle biopsies were taken from the vastus lateralis muscle using the Bergstroem technique.
Tissue was snap frozen in liquid nitrogen-cooled isopentane and kept frozen at -70 deg C.


title: Ho982 1h 2


title: Ho981 8h 2


title: Ho981 pre 2


title: Aorta Eln+/+ AO_WT_4

value: aorta

value: Elastin +/+

value: 30 days


title: Ho981 24h 2


title: Ho982 1h 1


title: Ho981 1h 2


title: Ho981 24h 1


title: Ho984 24h 2


title: Ho981 pre 1

label_protocol: 2.5 micogram totla RNA was reverse-transcribed using Superscript II (Invitrogen, Basel, Switzerland). Standardized amounts of [alpha-32P-dCTP] were used per reaction. Radiolabelled cDNA target was purified from the reaction using the supplied cartridge (BD Biosciences).


title: Ho981 8h 1


title: Ho981 1h 1


title: LNCaP_100pM

status: Public on Nov 01 2009

first: Shawn

middle: E

last: Lupold

address: 600 N Wolfe St

department: Urology

institute: Johns Hopkins University School of Medicine

hyb_protocol: 10 micrograms of RNA was Cy3-labeled and hybridized to custum microarrays.  The custom microarrays contained oligonucleotide probes complementary to 474 human miRNAs were synthesized by Combimatrix.  Probes containing 2 mismatches were included for all miRNAs.  Arrays were pre-hybridized at 37 degrees for 1 hour in 3X SSC, 0.1% SDS, 0.2% BSA.  Labeled RNA was hybridized to arrays at 37 degrees overnight in 400mM Na2HPO4 (pH 7.0), 0.8% BSA, 5% SDS, and 12% formamide.  Arrays were washed once at room temperature in 2X SSC, 0.25% SDS, 3 times at room temperature in 1.6X SSC, and twice in ice-cold 0.8X SSC.

scan_protocol: Hybridized arrays were scanned using a GenePix 4000B microarray scanner (Axon) and signal intensities were extracted using the Combimatrix Microarray Imager software.

data_processing: The background value was determined by calculating the median signal from the mismatch probes and this value was subtracted from all perfect match probes.  Signals that were less than 1.5 times background were removed and datasets were median centered prior to calculating fold-change values.

source_name: treated tissue culture cells

label_protocol: Total RNA was labeled with Cy3 as described (Thomson et al., 2004)

growth_protocol: 3.7 million LNCaP cells were seeded in 75-cm flasks.

treatment_protocol: 24 hours after maintaining the cells in androgen-free media (media supplemented with 10 % charcoal-stripped serum (Hyclone)), cells were treated with 0, 0.1, 1 or 10 nM R1881 and total RNA isolated with Trizol reagent (InVitrogen).

value: LNCaP

tag: cells

value: human prostate adenocarcinoma cells


title: LNCaP_1nM

description: 10 micrograms of RNA was Cy3-labeled and hybridized to custum microarrays.  The custom microarrays contained oligonucleotide probes complementary to 474 human miRNAs were synthesized by Combimatrix

extract_protocol: total RNA isolated with Trizol reagent (InVitrogen).


title: LNCaP_0nM

source_name: untreated tissue culture cells


title: LNCaP_10nM


title: LAPC4_0nM

growth_protocol: 3.7 million LAPC-4 cells were seeded in 75-cm flasks.

value: human prostate cancer cells


title: LAPC4_100pM


title: LAPC4_10nM


title: PS Chip#10

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

description: PS Chip#10.CEL

hyb_protocol: Affymetrix protocol

scan_protocol: Hewlett–Packard Gene Array Scanner

data_processing: GCRMA (using gcrma package from R/Bioconductor). Each platform was preprocess separately, then merged. An extra quantile normalization was needed to normalized across platforms (matrix of additionally-normalized data is available as GSE16161 supplementary file, GSE16161_QuantNormAcrossPlatform.txt).

source_name: Psoriasis, Leasional, Patient J

label_protocol: Affymetrix protocol

extract_protocol: Qiagen RNeasy Kit protocol

value: skin biopsy

tag: individual

value: Patient J

tag: condition

value: Psoriasis


title: AD Chip#5

description: AD Chip#5.CEL

source_name: AD, Leasional, Patient 0007

value: Patient 0007

value: atopic dermatitis (AD)


title: PS Chip#11

description: PS Chip#11.CEL

source_name: Psoriasis, Leasional, Patient K

value: Patient K


title: AD Chip#4

description: AD Chip#4.CEL

source_name: AD, Leasional, Patient 0006

value: Patient 0006


title: PS Chip#9

description: PS Chip#9.CEL

source_name: Psoriasis, Leasional, Patient I

value: Patient I


title: AD Chip#6

description: AD Chip#6.CEL

source_name: AD, Leasional, Patient 0008

value: Patient 0008


title: PS Chip#13

description: PS Chip#13.CEL

source_name: Psoriasis, Leasional, Patient M

value: Patient M


title: PS Chip#14

description: PS Chip#14.CEL

source_name: Psoriasis, Leasional, Patient N

value: Patient N


title: AD Chip#9

description: AD Chip#9.CEL

source_name: AD, Leasional, Patient 0011

value: Patient 0011


title: Ho984 pre 2

value: Resting biopsy before 30 minutes of endurance exercise in the trained state.


title: AD Chip#7

description: AD Chip#7.CEL

source_name: AD, Leasional, Patient 0009

value: Patient 0009


title: PS Chip#7

description: PS Chip#7.CEL

source_name: Psoriasis, Leasional, Patient G

value: Patient G


title: Normal Chip#9

description: Normal Chip#9.CEL

source_name: Normal, ma, Patient 10

value: Patient 10

value: Normal


title: AD Chip#2

description: AD Chip#2.CEL

source_name: AD, Leasional, Patient 0004

value: skin biopsy

value: Patient 0004


title: PS Chip#6

description: PS Chip#6.CEL

source_name: Psoriasis, Leasional, Patient F

value: Patient F

value: Psoriasis


title: PS Chip#8

description: PS Chip#8.CEL

source_name: Psoriasis, Leasional, Patient H

value: Patient H


title: PS Chip#5

description: PS Chip#5.CEL

source_name: Psoriasis, Leasional, Patient E

value: Patient E


title: PS Chip#2

description: PS Chip#2.CEL

source_name: Psoriasis, Leasional, Patient B

value: Patient B


title: AD Chip#8

description: AD Chip#8.CEL

source_name: AD, Leasional, Patient 0010

value: Patient 0010

value: atopic dermatitis (AD)


title: PS Chip#3

description: PS Chip#3.CEL

source_name: Psoriasis, Leasional, Patient C

value: Patient C


title: AD Chip#3

description: AD Chip#3.CEL

source_name: AD, Leasional, Patient 0005

value: Patient 0005


title: AD Chip#1

description: AD Chip#1.CEL

source_name: AD, Leasional, Patient 0002

value: Patient 0002


title: PS Chip#15

description: PS Chip#15.CEL

source_name: Psoriasis, Leasional, Patient O

value: Patient O


title: PS Chip#1

description: PS Chip#1.CEL

source_name: Psoriasis, Leasional, Patient A

value: Patient A


title: PS Chip#4

description: PS Chip#4.CEL

source_name: Psoriasis, Leasional, Patient D

value: Patient D


title: KMS11-Ethanol-rep2

source_name: KMS11 cells, ethanol treated

value: multiple myeloma

value: statin sensitive

value: ethanol


title: LAPC4_1nM

source_name: treated tissue culture cells

value: human prostate cancer cells


title: Olfactory_Epithelium_Rat-32

city: RENNES

first: Francis

last: Galibert

address: 2 av du Pr Léon Bernard

department: Génétique et Developpement

institute: CNRS UMR6061/Université Rennes1

hyb_protocol: Hybridization was performed using the Agilent Gene Expression Hybridization kit (p/n 5188-5242), following the manufacturer’s instructions. Briefly, 1650 ng of labeled cRNA was mixed with Hybridization Buffer and Blocking Agent and subjected to fragmentation (by incubation for 30 min at 60°C in the dark). Hybridizations onto 4x44K Whole Rat Genome 60-mer oligonucleotide microarrays (G4131F) (Agilent Technologies) were performed in a rotary oven (65°C, 17 h and 10 rpm) in the dark. Slides were disassembled and washed in Gene Expression wash Buffers I and II according to the manufacturer’s instructions, and dried using a nitrogen-filled air gun before scanning.

scan_protocol: Microarrays were scanned with a dynamic autofocus microarray scanner (Agilent DNA Microarray Scanner), using Agilent parameters. Feature Extraction software version 9.5 was used to extract and analyze the signals.

data_processing: Array results were analyzed using GeneSpring GX software version 7.3 (Agilent Technologies), via the Enhanced Agilent Feature Extraction Import Preprocessor.  Data were normalized in two steps using the algorithms supplied with the Feature Extraction software. Data were first transformed to convert any negative value to 0.01, then normalization was performed by using a per-chip 50th percentile method that normalizes each chip to its median, allowing comparison between chips. A second normalization step was applied to the results for each gene across all the arrays in the study (normalize to median): the median of all the values obtained for a given gene was calculated and used as the normalization standard for that gene, such that, regardless of absolute differences in the expression of the various genes, they are placed on the same scale for comparison.

source_name: Olfactory epithelium of rat 32 (litter4)

label_protocol: RNA samples were labeled using the Agilent Low RNA Input Fluorescent Linear Amplification kit (p/n 5184-3523) according to the manufacturer’s instructions. Briefly, 350 ng of total RNA was used as template and copied into cDNA by reverse transcription and concomitant amplification with T7-polymerase; cyanine-3 (Cy3)-labeled CTP was used for labeling. Cy3 labeling was monitored with a Nanodrop ND-1000 spectrophotometer and was found to be between 1.2 and 1.9 pmol/μl.

extract_protocol: Total RNA was isolated using the Nucleospin RNA kit according to the manufacturer’s (Macherey-Nagel) instructions, which included an in-column DNase treatment before RNA elution to ensure the absence of genomic DNA. Recovered RNA was quantified using a Nanodrop ND-1000 spectrophotometer (NanoDrop Technologies), and RNA integrity was assessed with RNA 6000 Nano LabChip kit using the Agilent 2100 Bioanalyzer (Agilent Technologies). Only RNA samples with an RNA Integrity Number (RIN) greater than 8.5 were used for further analysis (RNA profiling analysis and semi quantitative reverse transcription PCR analysis). Because of the application of this strict quality threshold, the left sample from one adult olfactory epithelium was not studied.

tag: strain

value: Brown Norway

value: Olfactory epithelium

tag: gender

value: Not known

tag: litter

value: 3-5 days


title: Olfactory_Epithelium_Rat-35

source_name: Olfactory epithelium of rat 35 (litter4)

tag: tissue


title: Olfactory_Epithelium_Rat-28

source_name: Olfactory epithelium of rat 28 (litter3)

tag: age


title: Olfactory_Epithelium_Rat-25

source_name: Olfactory epithelium of rat 25 (litter2)


title: Olfactory_Epithelium_Rat-29

source_name: Olfactory epithelium of rat 29 (litter3)


title: Olfactory_Epithelium_Rat-23

source_name: Olfactory epithelium of rat 23 (litter2)


title: Olfactory_Epithelium_Rat-30

source_name: Olfactory epithelium of rat 30 (litter3)


title: Olfactory_Epithelium_Rat-26

source_name: Olfactory epithelium of rat 26 (litter3)


title: Olfactory_Epithelium_Rat-27

source_name: Olfactory epithelium of rat 27 (litter3)


title: Olfactory_Epithelium_Rat-24

source_name: Olfactory epithelium of rat 24 (litter2)


title: Olfactory_Epithelium_Rat-22

source_name: Olfactory epithelium of rat 22 (litter2)


title: Olfactory_Epithelium_Rat-18A

source_name: Olfactory epithelium of rat 18, nostril A

value: Male

value: 22 months


title: Olfactory_Epithelium_Rat-34

source_name: Olfactory epithelium of rat 34 (litter4)


title: Olfactory_Epithelium_Rat-33

source_name: Olfactory epithelium of rat 33 (litter4)


title: Olfactory_Epithelium_Rat-21

source_name: Olfactory epithelium of rat 21 (litter2)


title: Olfactory_Epithelium_Rat-20B

source_name: Olfactory epithelium of rat 20, nostril B


title: Olfactory_Epithelium_Rat-19B

source_name: Olfactory epithelium of rat 19, nostril B


title: Olfactory_Epithelium_Rat-18B

source_name: Olfactory epithelium of rat 18, nostril B


title: Olfactory_Epithelium_Rat-17B

source_name: Olfactory epithelium of rat 17, nostril B


title: Olfactory_Epithelium_Rat-16B

source_name: Olfactory epithelium of rat 16, nostril B

value: 9 weeks


title: Olfactory_Epithelium_Rat-17A

source_name: Olfactory epithelium of rat 17, nostril A


title: Olfactory_Epithelium_Rat-19A

source_name: Olfactory epithelium of rat 19, nostril A


title: Olfactory_Epithelium_Rat-31

source_name: Olfactory epithelium of rat 31 (litter4)


title: Olfactory_Epithelium_Rat-20A

source_name: Olfactory epithelium of rat 20, nostril A


title: Olfactory_Epithelium_Rat-16A

source_name: Olfactory epithelium of rat 16, nostril A


title: Olfactory_Epithelium_Rat-15A

source_name: Olfactory epithelium of rat 15, nostril A


title: Olfactory_Epithelium_Rat-15B

source_name: Olfactory epithelium of rat 15, nostril B


title: Olfactory_Epithelium_Rat-11

source_name: Olfactory epithelium of rat 11 (litter1)


title: Olfactory_Epithelium_Rat-9

source_name: Olfactory epithelium of rat 9 (litter1)


title: PS Chip#12

description: PS Chip#12.CEL

source_name: Psoriasis, Leasional, Patient L

value: skin biopsy

value: Patient L

value: Psoriasis


title: Olfactory_Epithelium_Rat-14A

source_name: Olfactory epithelium of rat 14, nostril A


title: Olfactory_Epithelium_Rat-12

source_name: Olfactory epithelium of rat 12 (litter1)


title: Olfactory_Epithelium_Rat-5B

source_name: Olfactory epithelium of rat 5, nostril B

extract_protocol: Total RNA was isolated using the Nucleospin RNA kit according to the manufacturer’s (Macherey-Nagel) instructions, which included an in-column DNase treatment before RNA elution to ensure the absence of genomic DNA. Recovered RNA was quantified using a Nanodrop ND-1000 spectrophotometer (NanoDrop Technologies), and RNA integrity was assessed with RNA 6000 Nano LabChip kit using the Agilent 2100 Bioanalyzer (Agilent Technologies). Only RNA samples with an RNA Integrity Number (RIN) greater than 8.5 were used for further analysis (RNA profiling analysis and semi-quantitative reverse transcription PCR analysis). Because of the application of this strict quality threshold, the left sample from one adult olfactory epithelium was not studied.

value: 6 weeks


title: Olfactory_Epithelium_Rat-8A

source_name: Olfactory epithelium of rat 8, nostril A

value: Female